We profiled the genes and novel transcripts expressed in male mouse embryonic gonads at E10.5 (embryonic day 10.5), E11.5, E12.5, E13.5, E15.5 and E17.5 with an average of 152K coverage for each of the SAGE libraries. The 6 transcriptomes gave a total of 45,000 known transcripts, 21,000 uncharacterized cDNAs, and 4000 novel transcripts. Among the 10 most abundantly expressed transcripts, 5 encoded ribosomal proteins, similar to that observed in human embryonic stem cells. Six of the most abundantly expressed transcripts including cytochrome b oxidase, subunit 5b (Cox5), cytochrome b-245, beta polypeptide (Cybb), tumor protein, translationally-controlled 1 (Tpt1), ribosomal protein L19 (Rpl19), ubiquitin A-52 residue ribosomal protein fusion product 1 (Uba52), and an uncharacterized cDNA, were also among the 10 most abundant transcripts in type A spermatogonia. Application of unsupervised clustering analysis to the embryonic gonad transcriptomes yielded distinct genomic fingerprints of two major stages in gonad development, namely early (E10.5-E12.5) and late (E13.5-E17.5) stages. [unreadable] [unreadable] To identify the chromosomal regions most active during gonad development, we created algorithms to assign the SAGE tags to the corresponding chromosomal position based on the Unigene assignments and displayed in chromosome graphic format using the completed mouse genome information. Consequently, a chromosome heatmap of embryonic gonad development was created in which chromosomal hotspots with significant changes at any time point of development were highlighted based on co-localization of gene expression. This chromosome heatmap will be useful for determining the importance of different regions at specific time point during the developmental process and the potential consequences due to chromosome duplication or deletion. Furthermore, the biological implication of significant chromosomal clusters can be extracted and further analyzed by linking to different mutation and functional annotation databases including Online Mendelian Inheritance in Man (OMIM) and EASE.